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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs11202607

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87967657 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.068951 (8658/125568, TOPMED)
T=0.067060 (8244/122934, ALFA Project)
T=0.06484 (2016/31092, GnomAD) (+ 16 more)
T=0.0789 (395/5008, 1000G)
T=0.0730 (327/4480, Estonian)
T=0.0633 (244/3854, ALSPAC)
T=0.0636 (236/3708, TWINSUK)
T=0.0785 (230/2930, KOREAN)
T=0.0849 (177/2084, HGDP_Stanford)
T=0.0795 (150/1886, HapMap)
T=0.0731 (134/1832, Korea1K)
T=0.088 (53/600, NorthernSweden)
T=0.086 (46/534, MGP)
T=0.120 (26/216, Qatari)
T=0.098 (21/214, Vietnamese)
C=0.451 (46/102, SGDP_PRJ)
T=0.10 (4/40, GENOME_DK)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : 3 Prime UTR Variant
Publications
7 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 10 NC_000010.11:g.87967657C>T
GRCh37.p13 chr 10 NC_000010.10:g.89727414C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.109219C>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.183446C>T
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 2 NM_001304718.2:c.*2185= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_001304717.5:c.*2185= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.*2185= N/A 3 Prime UTR Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 323753 )
ClinVar Accession Disease Names Clinical Significance
RCV000314944.1 PTEN hamartoma tumor syndrome Benign

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 216608 C=0.932191 T=0.067809
European Sub 190544 C=0.932094 T=0.067906
African Sub 9718 C=0.9589 T=0.0411
African Others Sub 348 C=0.954 T=0.046
African American Sub 9370 C=0.9591 T=0.0409
Asian Sub 746 C=0.891 T=0.109
East Asian Sub 600 C=0.888 T=0.112
Other Asian Sub 146 C=0.904 T=0.096
Latin American 1 Sub 784 C=0.927 T=0.073
Latin American 2 Sub 2842 C=0.8374 T=0.1626
South Asian Sub 5042 C=0.9582 T=0.0418
Other Sub 6932 C=0.9222 T=0.0778


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.931049 T=0.068951
ALFA Total Global 122934 C=0.932940 T=0.067060
ALFA European Sub 107540 C=0.932453 T=0.067547
ALFA African Sub 5918 C=0.9557 T=0.0443
ALFA South Asian Sub 4894 C=0.9583 T=0.0417
ALFA Other Sub 2444 C=0.9051 T=0.0949
ALFA Latin American 2 Sub 1374 C=0.8319 T=0.1681
ALFA Latin American 1 Sub 502 C=0.942 T=0.058
ALFA Asian Sub 262 C=0.916 T=0.084
gnomAD - Genomes Global Study-wide 31092 C=0.93516 T=0.06484
gnomAD - Genomes European Sub 18678 C=0.93329 T=0.06671
gnomAD - Genomes African Sub 8670 C=0.9589 T=0.0411
gnomAD - Genomes East Asian Sub 1556 C=0.8792 T=0.1208
gnomAD - Genomes Other Sub 1072 C=0.9179 T=0.0821
gnomAD - Genomes American Sub 828 C=0.849 T=0.151
gnomAD - Genomes Ashkenazi Jewish Sub 288 C=0.955 T=0.045
1000Genomes Global Study-wide 5008 C=0.9211 T=0.0789
1000Genomes African Sub 1322 C=0.9539 T=0.0461
1000Genomes East Asian Sub 1008 C=0.8641 T=0.1359
1000Genomes Europe Sub 1006 C=0.9235 T=0.0765
1000Genomes South Asian Sub 978 C=0.968 T=0.032
1000Genomes American Sub 694 C=0.872 T=0.128
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9270 T=0.0730
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9367 T=0.0633
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9364 T=0.0636
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9215 T=0.0785
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.9151 T=0.0849
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.900 T=0.100
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.942 T=0.058
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.920 T=0.080
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.938 T=0.062
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.979 T=0.021
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.778 T=0.222
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.93 T=0.07
HapMap Global Study-wide 1886 C=0.9205 T=0.0795
HapMap American Sub 770 C=0.926 T=0.074
HapMap African Sub 688 C=0.914 T=0.086
HapMap Asian Sub 254 C=0.921 T=0.079
HapMap Europe Sub 174 C=0.920 T=0.080
Korean Genome Project KOREAN Study-wide 1832 C=0.9269 T=0.0731
Northern Sweden ACPOP Study-wide 600 C=0.912 T=0.088
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.914 T=0.086
Qatari Global Study-wide 216 C=0.880 T=0.120
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.902 T=0.098
SGDP_PRJ Global Study-wide 102 C=0.451 T=0.549
The Danish reference pan genome Danish Study-wide 40 C=0.90 T=0.10
Siberian Global Study-wide 6 C=0.5 T=0.5
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T
GRCh38.p12 chr 10 NC_000010.11:g.87967657= NC_000010.11:g.87967657C>T
GRCh37.p13 chr 10 NC_000010.10:g.89727414= NC_000010.10:g.89727414C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.109219= NG_007466.2:g.109219C>T
PTEN transcript variant 1 NM_000314.8:c.*2185= NM_000314.8:c.*2185C>T
PTEN transcript variant 1 NM_000314.7:c.*2185= NM_000314.7:c.*2185C>T
PTEN transcript variant 1 NM_000314.6:c.*2185= NM_000314.6:c.*2185C>T
PTEN transcript NM_000314.4:c.*2185= NM_000314.4:c.*2185C>T
PTEN transcript variant 1 NM_001304717.5:c.*2185= NM_001304717.5:c.*2185C>T
PTEN transcript variant 1 NM_001304717.4:c.*2185= NM_001304717.4:c.*2185C>T
PTEN transcript variant 1 NM_001304717.3:c.*2185= NM_001304717.3:c.*2185C>T
PTEN transcript variant 1 NM_001304717.2:c.*2185= NM_001304717.2:c.*2185C>T
PTEN transcript variant 2 NM_001304718.2:c.*2185= NM_001304718.2:c.*2185C>T
PTEN transcript variant 2 NM_001304718.1:c.*2185= NM_001304718.1:c.*2185C>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.183446= NW_013171807.1:g.183446C>T
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

86 SubSNP, 18 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16083271 Feb 27, 2004 (120)
2 SC_SNP ss18439187 Feb 27, 2004 (120)
3 EGP_SNPS ss38349857 Mar 15, 2006 (126)
4 SI_EXO ss61705810 Oct 16, 2006 (127)
5 ILLUMINA ss66926550 Dec 02, 2006 (127)
6 ILLUMINA ss67079284 Dec 02, 2006 (127)
7 ILLUMINA ss68103670 Dec 12, 2006 (127)
8 ILLUMINA ss70524471 May 24, 2008 (130)
9 ILLUMINA ss71054118 May 18, 2007 (127)
10 ILLUMINA ss74917282 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss85086931 Dec 14, 2007 (130)
12 ILLUMINA ss152963051 Dec 01, 2009 (131)
13 ILLUMINA ss159170354 Dec 01, 2009 (131)
14 ILLUMINA ss159969290 Dec 01, 2009 (131)
15 ILLUMINA ss171158564 Jul 04, 2010 (132)
16 1000GENOMES ss235274509 Jul 15, 2010 (132)
17 1000GENOMES ss241961759 Jul 15, 2010 (132)
18 ILLUMINA ss244272001 Jul 04, 2010 (132)
19 GMI ss280714863 May 04, 2012 (137)
20 GMI ss286235669 Apr 25, 2013 (138)
21 ILLUMINA ss479495895 May 04, 2012 (137)
22 ILLUMINA ss479499807 May 04, 2012 (137)
23 ILLUMINA ss479942940 Sep 08, 2015 (146)
24 ILLUMINA ss484547289 May 04, 2012 (137)
25 ILLUMINA ss536686110 Sep 08, 2015 (146)
26 SSMP ss657123270 Apr 25, 2013 (138)
27 ILLUMINA ss778755854 Sep 08, 2015 (146)
28 ILLUMINA ss782720307 Sep 08, 2015 (146)
29 ILLUMINA ss783687891 Sep 08, 2015 (146)
30 ILLUMINA ss831971868 Sep 08, 2015 (146)
31 ILLUMINA ss832682895 Jul 13, 2019 (153)
32 ILLUMINA ss834215563 Sep 08, 2015 (146)
33 EVA-GONL ss987754612 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1077180490 Aug 21, 2014 (142)
35 1000GENOMES ss1338439654 Aug 21, 2014 (142)
36 DDI ss1426397491 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1575269335 Apr 01, 2015 (144)
38 EVA_DECODE ss1597427372 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1625094830 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1668088863 Apr 01, 2015 (144)
41 EVA_MGP ss1711264015 Apr 01, 2015 (144)
42 EVA_SVP ss1713198921 Apr 01, 2015 (144)
43 ILLUMINA ss1751985443 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1931122886 Feb 12, 2016 (147)
45 GENOMED ss1967189171 Jul 19, 2016 (147)
46 JJLAB ss2026289193 Sep 14, 2016 (149)
47 USC_VALOUEV ss2154564584 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2176768849 Dec 20, 2016 (150)
49 TOPMED ss2339872340 Dec 20, 2016 (150)
50 ILLUMINA ss2632742306 Nov 08, 2017 (151)
51 GRF ss2698815896 Nov 08, 2017 (151)
52 ILLUMINA ss2710716510 Nov 08, 2017 (151)
53 GNOMAD ss2891608618 Nov 08, 2017 (151)
54 SWEGEN ss3006890001 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3026934160 Nov 08, 2017 (151)
56 TOPMED ss3126322888 Nov 08, 2017 (151)
57 CSHL ss3349240484 Nov 08, 2017 (151)
58 ILLUMINA ss3626499460 Oct 12, 2018 (152)
59 ILLUMINA ss3630766109 Oct 12, 2018 (152)
60 ILLUMINA ss3632958425 Oct 12, 2018 (152)
61 ILLUMINA ss3633656006 Oct 12, 2018 (152)
62 ILLUMINA ss3634415191 Oct 12, 2018 (152)
63 ILLUMINA ss3635348313 Oct 12, 2018 (152)
64 ILLUMINA ss3636098996 Oct 12, 2018 (152)
65 ILLUMINA ss3637099016 Oct 12, 2018 (152)
66 ILLUMINA ss3637864282 Oct 12, 2018 (152)
67 ILLUMINA ss3638948113 Oct 12, 2018 (152)
68 ILLUMINA ss3639785516 Oct 12, 2018 (152)
69 ILLUMINA ss3640122532 Oct 12, 2018 (152)
70 ILLUMINA ss3641004742 Oct 12, 2018 (152)
71 ILLUMINA ss3641299064 Oct 12, 2018 (152)
72 ILLUMINA ss3642866533 Oct 12, 2018 (152)
73 ILLUMINA ss3643838078 Oct 12, 2018 (152)
74 OMUKHERJEE_ADBS ss3646412928 Oct 12, 2018 (152)
75 EGCUT_WGS ss3674299760 Jul 13, 2019 (153)
76 EVA_DECODE ss3690370101 Jul 13, 2019 (153)
77 ACPOP ss3737543979 Jul 13, 2019 (153)
78 ILLUMINA ss3744716163 Jul 13, 2019 (153)
79 EVA ss3748412302 Jul 13, 2019 (153)
80 ILLUMINA ss3772216546 Jul 13, 2019 (153)
81 KHV_HUMAN_GENOMES ss3813779709 Jul 13, 2019 (153)
82 EVA ss3825779613 Apr 26, 2020 (154)
83 HGDP ss3847394455 Apr 26, 2020 (154)
84 SGDP_PRJ ss3874733788 Apr 26, 2020 (154)
85 KRGDB ss3922849710 Apr 26, 2020 (154)
86 KOGIC ss3968370719 Apr 26, 2020 (154)
87 1000Genomes NC_000010.10 - 89727414 Oct 12, 2018 (152)
88 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89727414 Oct 12, 2018 (152)
89 Genetic variation in the Estonian population NC_000010.10 - 89727414 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000010.10 - 89727414 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000010.10 - 89727414 Jul 13, 2019 (153)
92 HGDP-CEPH-db Supplement 1 NC_000010.9 - 89717394 Apr 26, 2020 (154)
93 HapMap NC_000010.11 - 87967657 Apr 26, 2020 (154)
94 KOREAN population from KRGDB NC_000010.10 - 89727414 Apr 26, 2020 (154)
95 Korean Genome Project NC_000010.11 - 87967657 Apr 26, 2020 (154)
96 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 89727414 Apr 26, 2020 (154)
97 Northern Sweden NC_000010.10 - 89727414 Jul 13, 2019 (153)
98 Qatari NC_000010.10 - 89727414 Apr 26, 2020 (154)
99 SGDP_PRJ NC_000010.10 - 89727414 Apr 26, 2020 (154)
100 Siberian NC_000010.10 - 89727414 Apr 26, 2020 (154)
101 TopMed NC_000010.11 - 87967657 Oct 12, 2018 (152)
102 UK 10K study - Twins NC_000010.10 - 89727414 Oct 12, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000010.10 - 89727414 Jul 13, 2019 (153)
104 dbGaP Population Frequency Project NC_000010.11 - 87967657 Apr 26, 2020 (154)
105 ClinVar RCV000314944.1 Oct 12, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs57796787 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638948113, ss3639785516, ss3643838078 NC_000010.8:89717393:C:T NC_000010.11:87967656:C:T (self)
72347, ss280714863, ss286235669, ss479495895, ss1597427372, ss1713198921, ss3642866533, ss3847394455 NC_000010.9:89717393:C:T NC_000010.11:87967656:C:T (self)
50864081, 28233939, 20038008, 2263953, 138963079, 30027104, 379775, 10828844, 13164816, 26750768, 7080938, 28233939, 6270206, ss235274509, ss241961759, ss479499807, ss479942940, ss484547289, ss536686110, ss657123270, ss778755854, ss782720307, ss783687891, ss831971868, ss832682895, ss834215563, ss987754612, ss1077180490, ss1338439654, ss1426397491, ss1575269335, ss1625094830, ss1668088863, ss1711264015, ss1751985443, ss1931122886, ss1967189171, ss2026289193, ss2154564584, ss2339872340, ss2632742306, ss2698815896, ss2710716510, ss2891608618, ss3006890001, ss3349240484, ss3626499460, ss3630766109, ss3632958425, ss3633656006, ss3634415191, ss3635348313, ss3636098996, ss3637099016, ss3637864282, ss3640122532, ss3641004742, ss3641299064, ss3646412928, ss3674299760, ss3737543979, ss3744716163, ss3748412302, ss3772216546, ss3825779613, ss3874733788, ss3922849710 NC_000010.10:89727413:C:T NC_000010.11:87967656:C:T (self)
RCV000314944.1, 457910, 24748720, 48131742, 647071544, ss2176768849, ss3026934160, ss3126322888, ss3690370101, ss3813779709, ss3968370719 NC_000010.11:87967656:C:T NC_000010.11:87967656:C:T (self)
ss16083271, ss18439187 NT_030059.11:8475929:C:T NC_000010.11:87967656:C:T (self)
ss61705810 NT_030059.12:8475929:C:T NC_000010.11:87967656:C:T (self)
ss38349857, ss66926550, ss67079284, ss68103670, ss70524471, ss71054118, ss74917282, ss85086931, ss152963051, ss159170354, ss159969290, ss171158564, ss244272001 NT_030059.13:40531877:C:T NC_000010.11:87967656:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

7 citations for rs11202607
PMID Title Author Year Journal
21093899 Endometrial cancer and genetic variation in PTEN, PIK3CA, AKT1, MLH1, and MSH2 within a population-based case-control study. Lacey JV Jr et al. 2011 Gynecologic oncology
21633361 Germ-line sequence variants of PTEN do not have an important role in hereditary and non-hereditary prostate cancer susceptibility. Xie CC et al. 2011 Journal of human genetics
22815832 Genetic variations in a PTEN/AKT/mTOR axis and prostate cancer risk in a Chinese population. Chen J et al. 2012 PloS one
23209702 A functional variant in the MTOR promoter modulates its expression and is associated with renal cell cancer risk. Cao Q et al. 2012 PloS one
24935469 The association of phosphatase and tensin homolog deleted on chromosome 10 polymorphisms and lifestyle habits with colorectal cancer risk in a Chinese population. Jing F et al. 2014 Tumour biology
26695147 PTEN polymorphisms contribute to clinical outcomes of advanced lung adenocarcinoma patients treated with platinum-based chemotherapy. Yang Y et al. 2016 Tumour biology
27876891 Genetic variations in the PI3K-PTEN-AKT-mTOR pathway are associated with distant metastasis in nasopharyngeal carcinoma patients treated with intensity-modulated radiation therapy. Guo Q et al. 2016 Scientific reports
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post565+e32b82c